It would have strained credulity to imagine during the orgy of terror unleashed by the US-backed coup on the other 9/11, in 1973. But 35 years after Richard Nixon gave the green light to the Chilean military to drown Salvador Allende's elected socialist government in blood, the net is finally closing on the man who personally machine-gunned to death one of the outstanding political songwriters of the 20th century.

This week, Judge Juan Eduardo Fuentes agreed to re-open the investigation into the murder of Victor Jara, Chile's most famous musician, killed by an army officer in the Estadio Chile stadium in Santiago, where he had been interned, beaten and tortured with 5,000 other "subversives" in the wake of General Pinochet's fascist takeover.

Last month, Fuentes closed the Jara case after finding a retired army colonel, Mario Manriquez, guilty of the murder as commanding officer at the stadium after the 1973 coup, while accepting that Manriquez had not pulled the trigger.

Within days, a concert was held in the same stadium where Jara was killed, now renamed Estadio Victor Jara, to protest at what is widely regarded as a military cover-up of those guilty of the atrocity. Among those taking part were the radical folk group Inti Illimani, who played with Jara, and the singer's widow, English-born choreographer Joan Turner Jara, who appealed to witnesses to come forward with information about the killer. Now the judge has reversed his earlier decision and agreed to look at 40 pieces of new evidence provided by the family and lawyers.

Jara famously had both his hands broken with soldiers' rifle butts so he could never play guitar again. "Sing now, if you can, you bastard," an officer spat at him. Despite four days of beatings, torture and food and sleep deprivation, Jara managed to sing a verse of the revolutionary anthem Venceremos to his fellow prisoners before being dragged away to be shot. His body, riddled with 44 bullets, was dumped in the street.

The military junta prohibited any public reference to the leftwing singer and his records were banned. But the same night, a TV technician risked his life by playing Jara's La Plegaria a un Labrador – a reworking of the Lord's Prayer, but addressed to a worker – over the soundtrack of a Hollywood film.

Former political prisoners say Jara's murder was carried out by a notoriously brutal officer nicknamed "El Principe" (The Prince) and the pressure is now on the military to reveal his identity – just as hundreds of former army and security officials are finally being prosecuted for crimes previously protected by the Pinochet regime's amnesty of the late 1970s.

More than 3,100 people were found by an official Chilean commission in the 1990s to have been killed by the Pinochet dictatorship in the aftermath of the 1973 coup, while tens of thousands were imprisoned and tortured – including Chile's current president, Michelle Bachelet.

But it is Jara – a writer of songs of great passion and poignancy, combining street language, traditional Andean music and the western pop idioms of the time – who has come to symbolise them all. His brutal martyrdom was foreshadowed in one of his most beautiful songs, Manifiesto: "A song has meaning when it beats in the veins of a man who will die singing, truthfully singing his song". And like that of Che Guevara, it has come to haunt both those who ordered it – and those who carried it out.